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Although optical alignment system for lithography can achieve very high resolution, for a lot of applications such as micro machining process, this kind of optical alignment system is either too expensive or not compatible with the equipment and the manufacturing process of interest. We propose a design of an ultra-high resolution alignment system utilizing a surface probe (SP) such as atomic force microscope (AFM) or scanning tunnelling microscope (STM) and an alignment marker. In order to realize the potential of utilizing surface probe microscope (SPM) as ultra-high resolution alignment system, one of the obstacles of poor definition of the alignment marker has to be overcome. Instead of a well defined points or lines, the alignment marker as fabricated by the available precision methods such as e beam or ion beam milling is still very large and very rough in comparison to the atomic dimension. A methodology is proposed to extract the alignment information from the alignment marker precisely. Using our method of extraction alignment information, our simulation study shows that alignment repeatability and accuracy in the order a few angstroms level can be achieved with our proposed alignment system.